R: Drop tips or extract clade from tree with mapped discrete...

drop.tip.simmap {phytools}

R Documentation

Drop tips or extract clade from tree with mapped discrete character

Description

This function drops one or multiple tips from the modified "phylo" object with a mapped binary or multistate trait (see read.simmap) while maintaining the matrix $mapped.edge and list of mappings by branch maps. This function is equivalent to drop.tip but for a tree with a mapped discrete character.

extract.clade.simmap is functionally equivalent to extract.clade but preserves discrete character mappings on the tree.

Usage

drop.tip.simmap(tree, tip)
extract.clade.simmap(tree, node)

Arguments

`tree`	a modified object of class `"phylo"` (see `read.simmap`).
`tip`	name or names of species to be dropped.
`node`	node number for the root node of the clade to be extracted.

Value

A modified object of class "phylo" containing the elements maps and $mapped.edge with the time spent in each state along each edge of the tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.